Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013838.1 Corchorus capsularis cultivar CVL-1 contig13859, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 36484
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:7876 original size:62 final size:62
Alignment explanation
Indices: 7800--7923 Score: 196
Period size: 62 Copynumber: 2.0 Consensus size: 62
7790 TTTGCTTGGT
* *
7800 AGTTTTAATCTTCCTCCTTGACCAAGTATAGCTCGCTTA-CCAAGTTTAGTCTCCATTGCCAA
1 AGTTTTAATCTTCCTCCTTGACCAAGTATAGCTCAC-CAGCCAAGTTTAGTCTCCATTGCCAA
* *
7862 AGTTTTAATCTTCCTCCTTGACCAAGTATAGCTTACCAGCTAAGTTTAGTCTCCATTGCCAA
1 AGTTTTAATCTTCCTCCTTGACCAAGTATAGCTCACCAGCCAAGTTTAGTCTCCATTGCCAA
7924 TAAAATCCCG
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
61 1 0.02
62 56 0.98
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (62 bp):
AGTTTTAATCTTCCTCCTTGACCAAGTATAGCTCACCAGCCAAGTTTAGTCTCCATTGCCAA
Found at i:9718 original size:12 final size:12
Alignment explanation
Indices: 9701--9731 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
9691 TACTGAACCA
9701 ATCCTCCTCAAT
1 ATCCTCCTCAAT
*
9713 ATCCTCTTCAAT
1 ATCCTCCTCAAT
9725 ATCCTCC
1 ATCCTCC
9732 AAAACTCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (12 bp):
ATCCTCCTCAAT
Found at i:11614 original size:122 final size:122
Alignment explanation
Indices: 11460--11735 Score: 355
Period size: 124 Copynumber: 2.3 Consensus size: 122
11450 AAATAATTAT
*
11460 AAAATAGAG-TTTTAGTAGAATAAAACTGTATATTAAAAAATTTTAATATATCCAAG-TTTT-T-
1 AAAATAGAGTTTTTAGTAGAATAAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTATA
* *
11521 AAAATAGTAAAATGCTAAAAATAAAATAATTATTATAAAAATATT-GAATTTAATTAAATG
66 AAAATAATAAAATGCTAAAAATAAAAT-A--ATTATAAAAATATTAG-ATTTAATTAAATA
** *
11581 AAAATAGAGTTTTTCTTAGAATAAAACTATATATTAAAAAGTTTTAATATATCCAAGTTTTTAAT
1 AAAATAGAGTTTTTAGTAGAATAAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTT-AT
* * * *
11646 CAAAAATAATAAAATGGTAAAAATTAAGTAATTATAAAGATATTAGATTTAATTAAATA
65 -AAAAATAATAAAATGCTAAAAATAAAATAATTATAAAAATATTAGATTTAATTAAATA
* *
11705 AAAATAGATTTTTTAGTAGAATGAAACTATA
1 AAAATAGAGTTTTTAGTAGAATAAAACTATA
11736 ATAGTTTAAG
Statistics
Matches: 134, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
121 9 0.07
122 43 0.32
123 4 0.03
124 52 0.39
125 2 0.01
126 1 0.01
127 23 0.17
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.37
Consensus pattern (122 bp):
AAAATAGAGTTTTTAGTAGAATAAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTATA
AAAATAATAAAATGCTAAAAATAAAATAATTATAAAAATATTAGATTTAATTAAATA
Found at i:14189 original size:21 final size:22
Alignment explanation
Indices: 14163--14207 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
14153 ATAAACTGAA
14163 TTGCTAAACACCGCCCC-CTTT
1 TTGCTAAACACCGCCCCACTTT
**
14184 TTGCTATTCACCGCCCCACTTT
1 TTGCTAAACACCGCCCCACTTT
14206 TT
1 TT
14208 ACATTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.16, C:0.40, G:0.09, T:0.36
Consensus pattern (22 bp):
TTGCTAAACACCGCCCCACTTT
Found at i:14458 original size:34 final size:32
Alignment explanation
Indices: 14387--14459 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 32
14377 TGTTGTCGGT
* *
14387 GCCGCCCCAGGAGGGCGGCATGCCGTGGCATA
1 GCCGCCCCAGGAGGGCGGCAAGCAGTGGCATA
*
14419 GCCGCCCCAGGAGGGCGGCAAGCTATTGGACATA
1 GCCGCCCCAGGAGGGCGGCAAGC-AGTGG-CATA
14453 GCCGCCC
1 GCCGCCC
14460 TCCTGGGGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 22 0.61
33 3 0.08
34 11 0.31
ACGTcount: A:0.18, C:0.36, G:0.37, T:0.10
Consensus pattern (32 bp):
GCCGCCCCAGGAGGGCGGCAAGCAGTGGCATA
Found at i:20042 original size:2 final size:2
Alignment explanation
Indices: 20035--20067 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20025 TCCCTACAGG
20035 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20068 ATTACATTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23360 original size:22 final size:21
Alignment explanation
Indices: 23299--23352 Score: 99
Period size: 21 Copynumber: 2.5 Consensus size: 21
23289 TGACCTGCCA
23299 CATGCCCGGCCATCACCATCG
1 CATGCCCGGCCATCACCATCG
23320 CATGCCCGGCCATCACCATCG
1 CATGCCCGGCCATCACCATCG
23341 CATGTCCCGGCC
1 CATG-CCCGGCC
23353 TTGCCCATGC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 25 0.78
22 7 0.22
ACGTcount: A:0.17, C:0.48, G:0.20, T:0.15
Consensus pattern (21 bp):
CATGCCCGGCCATCACCATCG
Found at i:24395 original size:20 final size:20
Alignment explanation
Indices: 24372--24436 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
24362 TCTAATATAT
24372 TATATATGATCATAAGTTTG
1 TATATATGATCATAAGTTTG
*
24392 TATATTTGAGTC-TAA-TATAT-
1 TATATATGA-TCATAAGT-T-TG
*
24412 TATATATGATCATAAGATTG
1 TATATATGATCATAAGTTTG
24432 TATAT
1 TATAT
24437 TACATTTTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
19 4 0.11
20 29 0.81
21 3 0.08
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (20 bp):
TATATATGATCATAAGTTTG
Found at i:24413 original size:40 final size:40
Alignment explanation
Indices: 24358--24437 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
24348 GTGAATGTCA
*
24358 TGAGTCTAATATATTATATATGATCATAAGTTTGTATATT
1 TGAGTCTAATATATTATATATGATCATAAGATTGTATATT
24398 TGAGTCTAATATATTATATATGATCATAAGATTGTATATT
1 TGAGTCTAATATATTATATATGATCATAAGATTGTATATT
24438 ACATTTTCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.46
Consensus pattern (40 bp):
TGAGTCTAATATATTATATATGATCATAAGATTGTATATT
Found at i:24631 original size:130 final size:131
Alignment explanation
Indices: 24490--24750 Score: 472
Period size: 130 Copynumber: 2.0 Consensus size: 131
24480 AACTTTTATA
24490 CGTAGGGTTTTTTTCTTTATATTTGATTACTTATTTTACTTATTACTATTATTTATTTGGGTAAA
1 CGTAGGGTTTTTTTCTTTATATTTGATTACTTATTTTACTTATTACTATTATTTATTTGGGTAAA
* *
24555 TTACATATATATACTCTGA-GGTTTGGGGTGAAATCAATATACTCCTGAGATTTAGAATTTAACA
66 TTACATATATATACCCT-ATGGTTTGGGGTGAAATCAATATACCCCTGAGATTTAGAATTTAACA
24619 CT
130 CT
*
24621 CGTA-GGTTTTTTTCTTTATATTTGATTACTTATTTTACTTCTTACTATTATTTATTTGGGTAAA
1 CGTAGGGTTTTTTTCTTTATATTTGATTACTTATTTTACTTATTACTATTATTTATTTGGGTAAA
24685 TTACATATATATACCCTATGGTTTGGGGTGAAATCAATATACCCCTGAGATTTAGAATTTAACAC
66 TTACATATATATACCCTATGGTTTGGGGTGAAATCAATATACCCCTGAGATTTAGAATTTAACAC
24750 T
131 T
24751 TAACTACCTT
Statistics
Matches: 126, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
129 1 0.01
130 121 0.96
131 4 0.03
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (131 bp):
CGTAGGGTTTTTTTCTTTATATTTGATTACTTATTTTACTTATTACTATTATTTATTTGGGTAAA
TTACATATATATACCCTATGGTTTGGGGTGAAATCAATATACCCCTGAGATTTAGAATTTAACAC
T
Found at i:27744 original size:27 final size:27
Alignment explanation
Indices: 27713--27769 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
27703 GACAAGGGGG
27713 ATGGGCCAAGCTCAAGTGCAGT-AGCAT
1 ATGGGCCAAGCTCAAGTGCA-TCAGCAT
27740 ATGGGCCAAGCTCAAGTGCATCAGCAT
1 ATGGGCCAAGCTCAAGTGCATCAGCAT
27767 ATG
1 ATG
27770 AGCCTGTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 1 0.03
27 28 0.97
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.19
Consensus pattern (27 bp):
ATGGGCCAAGCTCAAGTGCATCAGCAT
Found at i:29384 original size:39 final size:39
Alignment explanation
Indices: 29341--29453 Score: 95
Period size: 39 Copynumber: 3.1 Consensus size: 39
29331 TAATCACATG
29341 TATAACTCCTAAATTACTTAAAATATTATTCCAAATTAA
1 TATAACTCCTAAATTACTTAAAATATTATTCCAAATTAA
* * * *
29380 TATAA-T--T-AA-T-C--AAATATCTTTAAT-CACA-T-G
1 TATAACTCCTAAATTACTTAAA-AT-ATTATTCCAAATTAA
29410 TATAACTCCTAAATTACTTAAAATATTATTCCAAATTAA
1 TATAACTCCTAAATTACTTAAAATATTATTCCAAATTAA
29449 TATAA
1 TATAA
29454 TTAATAGGTA
Statistics
Matches: 53, Mismatches: 8, Indels: 26
0.61 0.09 0.30
Matches are distributed among these distances:
30 5 0.09
31 5 0.09
32 5 0.09
33 6 0.11
34 3 0.06
35 3 0.06
36 6 0.11
37 5 0.09
38 5 0.09
39 10 0.19
ACGTcount: A:0.46, C:0.14, G:0.01, T:0.39
Consensus pattern (39 bp):
TATAACTCCTAAATTACTTAAAATATTATTCCAAATTAA
Found at i:29399 original size:69 final size:69
Alignment explanation
Indices: 29320--29458 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
29310 CTATTATTGC
29320 TCAAATATCTTTAATCACATGTATAACTCCTAAATTACTTAAAATATTATTCCAAATTAATATAA
1 TCAAATATCTTTAATCACATGTATAACTCCTAAATTACTTAAAATATTATTCCAAATTAATATAA
29385 TTAA
66 TTAA
29389 TCAAATATCTTTAATCACATGTATAACTCCTAAATTACTTAAAATATTATTCCAAATTAATATAA
1 TCAAATATCTTTAATCACATGTATAACTCCTAAATTACTTAAAATATTATTCCAAATTAATATAA
29454 TTAA
66 TTAA
29458 T
1 T
29459 AGGTATATAC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.45, C:0.14, G:0.01, T:0.40
Consensus pattern (69 bp):
TCAAATATCTTTAATCACATGTATAACTCCTAAATTACTTAAAATATTATTCCAAATTAATATAA
TTAA
Found at i:29502 original size:2 final size:2
Alignment explanation
Indices: 29495--29525 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29485 TTCCTTTCTA
29495 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29526 ATTGATTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34557 original size:55 final size:56
Alignment explanation
Indices: 34490--34603 Score: 149
Period size: 55 Copynumber: 2.1 Consensus size: 56
34480 TAAATAATTA
**
34490 TTTAGAAATTAAGGTCAAGATGAGTCACTAACTC-TTTTGAAGGTTTACAAATTCT
1 TTTAGAAATTAAGGTCAAGACAAGTCACTAACTCTTTTTGAAGGTTTACAAATTCT
* ** * * *
34545 TTTAGGAATTAAGGTCAAGACAAGTCGTTCACTCTTTTTGAAGGTTTGCGAATTCT
1 TTTAGAAATTAAGGTCAAGACAAGTCACTAACTCTTTTTGAAGGTTTACAAATTCT
34601 TTT
1 TTT
34604 CCCCAGAGTT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
55 28 0.56
56 22 0.44
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (56 bp):
TTTAGAAATTAAGGTCAAGACAAGTCACTAACTCTTTTTGAAGGTTTACAAATTCT
Found at i:35738 original size:15 final size:16
Alignment explanation
Indices: 35712--35741 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35702 TATTTTCCTT
35712 TTTTGTTTCTTTTCTA
1 TTTTGTTTCTTTTCTA
35728 TTTTG-TTCTTTTCT
1 TTTTGTTTCTTTTCT
35742 CCCTTTTGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.03, C:0.13, G:0.07, T:0.77
Consensus pattern (16 bp):
TTTTGTTTCTTTTCTA
Done.